OpenRaiser/Intern-Atlas huggingface dataset:
Domain-Adversarial Neural Network and Explainable AI for Reducing Tissue-of-Origin Signal in Pan-cancer Mortality Classification
Venue: arXiv cs.LG 2025
Year: 2025

Tissue-of-origin signals dominate pan-cancer gene expression, often obscuring molecular features linked to patient survival. This hampers the discovery of generalizable biomarkers, as models tend to overfit tissue-specific patterns rather than capture survival-relevant signals. To address this, we propose a Domain-Adversarial Neural Network (DANN) trained on TCGA RNA-seq data to learn representations less biased by tissue and more focused on survival. Identifying tissue-independent genetic profiles is key to revealing core cancer programs. We assess the DANN using: (1) Standard SHAP, based on the original input space and DANN's mortality classifier; (2) A layer-aware strategy applied to hidden activations, including an unsupervised manifold from raw activations and a supervised manifold from mortality-specific SHAP values. Standard SHAP remains confounded by tissue signals due to biases inherent in its computation. The raw activation manifold was dominated by high-magnitude activations, which masked subtle tissue and mortality-related signals. In contrast, the layer-aware SHAP manifold offers improved low-dimensional representations of both tissue and mortality signals, independent of activation strength, enabling subpopulation stratification and pan-cancer identification of survival-associated genes.
Patch and Shuffle: A Preprocessing Technique for Texture Classification in Autonomous Cementitious Fabrication
Venue: arXiv cs.CV 2025
Year: 2025

Autonomous fabrication systems are transforming construction and manufacturing, yet they remain vulnerable to print errors. Texture classification is a key component of computer vision systems that enable real-time monitoring and adjustment during cementitious fabrication. Traditional classification methods often rely on global image features, which can bias the model toward semantic content rather than low-level textures. In this paper, we introduce a novel preprocessing technique called "patch and shuffle," which segments input images into smaller patches, shuffles them, and reconstructs a jumbled image before classification. This transformation removes semantic context, forcing the classifier to rely on local texture features. We evaluate this approach on a dataset of extruded cement images, using a ResNet-18-based architecture. Our experiments compare the patch and shuffle method to a standard pipeline, holding all other factors constant. Results show a significant improvement in accuracy: the patch and shuffle model achieved 90.64% test accuracy versus 72.46% for the baseline. These findings suggest that disrupting global structure enhances performance in texture-based classification tasks. This method has implications for broader vision tasks where low-level features matter more than high-level semantics. The technique may improve classification in applications ranging from fabrication monitoring to medical imaging.
MultiLoKo: a multilingual local knowledge benchmark for LLMs spanning 31 languages
Venue: arXiv cs.CL 2025
Year: 2025

We present MultiLoKo, a new benchmark for evaluating multilinguality in LLMs covering 31 languages. MultiLoKo consists of three partitions: a main partition consisting of 500 questions per language, separately sourced to be locally relevant to the specific language, and two translated partitions, containing human-authored translations from 30 non-English languages to English and vice versa. For comparison, we also release corresponding machine-authored translations. The data is equally distributed over two splits: a dev split and a blind, out-of-distribution test split. MultiLoKo can be used to study a variety of questions regarding the multilinguality of LLMs as well as meta-questions about multilingual benchmark creation. We compute MultiLoKo scores for 11 base and chat models marketed to be multilingual and study their average performance, their performance parity across languages, how much their ability to answer questions depends on the question language, and which languages are most difficult. None of the models we studied performs well on MultiLoKo, as indicated by low average scores as well as large differences between the best and worst scoring languages. Furthermore, we find a substantial effect of the question language, indicating sub-optimal knowledge transfer between languages. Lastly, we find that using local vs English-translated data can result in differences more than 20 points for the best performing models, drastically change the estimated difficulty of some languages. For using machines instead of human translations, we find a weaker effect on ordering of language difficulty, a larger difference in model rankings, and a substantial drop in estimated performance for all models.
DICE: A Framework for Dimensional and Contextual Evaluation of Language Models
Venue: arXiv cs.CL 2025
Year: 2025

Language models (LMs) are increasingly being integrated into a wide range of applications, yet the modern evaluation paradigm does not sufficiently reflect how they are actually being used. Current evaluations rely on benchmarks that often lack direct applicability to the real-world contexts in which LMs are being deployed. To address this gap, we propose Dimensional and Contextual Evaluation (DICE), an approach that evaluates LMs on granular, context-dependent dimensions. In this position paper, we begin by examining the insufficiency of existing LM benchmarks, highlighting their limited applicability to real-world use cases. Next, we propose a set of granular evaluation parameters that capture dimensions of LM behavior that are more meaningful to stakeholders across a variety of application domains. Specifically, we introduce the concept of context-agnostic parameters - such as robustness, coherence, and epistemic honesty - and context-specific parameters that must be tailored to the specific contextual constraints and demands of stakeholders choosing to deploy LMs into a particular setting. We then discuss potential approaches to operationalize this evaluation framework, finishing with the opportunities and challenges DICE presents to the LM evaluation landscape. Ultimately, this work serves as a practical and approachable starting point for context-specific and stakeholder-relevant evaluation of LMs.
Staggering and Fragmentation for Improved Large Message Handling in libp2p GossipSub
Venue: arXiv cs.NI 2025
Year: 2025

The libp2p GossipSub protocol leverages a full-message mesh with a lower node degree and a more densely connected metadata-only (gossip) mesh. This combination allows an efficient dissemination of messages in unstructured peer-to-peer (P2P) networks. However, GossipSub needs to consider message size, which is crucial for the efficient operation of many applications, such as handling large Ethereum blocks. This paper proposes modifications to improve GossipSub's performance when transmitting large messages. We evaluate the proposed improvements using the shadow simulator. Our results show that the proposed improvements significantly enhance GossipSub's performance for large message transmissions in sizeable networks.
Ctrl-Z: Controlling AI Agents via Resampling
Venue: arXiv cs.LG 2025
Year: 2025

Control evaluations measure whether monitoring and security protocols for AI systems prevent intentionally subversive AI models from causing harm. Our work presents the first control evaluation performed in an agent environment. We construct BashBench, a dataset of 257 challenging multi-step system administration tasks, and evaluate whether various safety measures can prevent an adversarially constructed AI agent from covertly downloading and executing malicious code in this environment. This multi-step setting introduces new attack and defense dynamics, which we investigate in order to design novel control protocols that prevent safety failures without hindering the ability of non-malicious agents to perform useful work. We introduce a class of control protocols called resample protocols that dynamically take additional samples of certain actions. We find these protocols significantly improve on existing techniques by selectively blocking the AI agent from executing suspicious code and incriminating the agent by generating additional examples of dangerous behavior. We measure the tradeoff between attack prevention and usefulness; our best protocol combines resampling with analysis of previous steps, reducing the success rate of attacks from 58% to 7% at a 5% cost to the performance of a non-malicious agent.
PG-DPIR: An efficient plug-and-play method for high-count Poisson-Gaussian inverse problems
Venue: arXiv cs.CV 2025
Year: 2025

Poisson-Gaussian noise describes the noise of various imaging systems thus the need of efficient algorithms for Poisson-Gaussian image restoration. Deep learning methods offer state-of-the-art performance but often require sensor-specific training when used in a supervised setting. A promising alternative is given by plug-and-play (PnP) methods, which consist in learning only a regularization through a denoiser, allowing to restore images from several sources with the same network. This paper introduces PG-DPIR, an efficient PnP method for high-count Poisson-Gaussian inverse problems, adapted from DPIR. While DPIR is designed for white Gaussian noise, a naive adaptation to Poisson-Gaussian noise leads to prohibitively slow algorithms due to the absence of a closed-form proximal operator. To address this, we adapt DPIR for the specificities of Poisson-Gaussian noise and propose in particular an efficient initialization of the gradient descent required for the proximal step that accelerates convergence by several orders of magnitude. Experiments are conducted on satellite image restoration and super-resolution problems. High-resolution realistic Pleiades images are simulated for the experiments, which demonstrate that PG-DPIR achieves state-of-the-art performance with improved efficiency, which seems promising for on-ground satellite processing chains.
Satellite Federated Fine-Tuning for Foundation Models in Space Computing Power Networks
Venue: arXiv cs.LG 2025
Year: 2025

Advancements in artificial intelligence (AI) and low-earth orbit (LEO) satellites have promoted the application of large remote sensing foundation models for various downstream tasks. However, direct downloading of these models for fine-tuning on the ground is impeded by privacy concerns and limited bandwidth. Satellite federated learning (FL) offers a solution by enabling model fine-tuning directly on-board satellites and aggregating model updates without data downloading. Nevertheless, for large foundation models, the computational capacity of satellites is insufficient to support effective on-board fine-tuning in traditional satellite FL frameworks. To address these challenges, we propose a satellite-ground collaborative federated fine-tuning framework. The key of the framework lies in how to reasonably decompose and allocate model components to alleviate insufficient on-board computation capabilities. During fine-tuning, satellites exchange intermediate results with ground stations or other satellites for forward propagation and back propagation, which brings communication challenges due to the special communication topology of space transmission networks, such as intermittent satellite-ground communication, short duration of satellite-ground communication windows, and unstable inter-orbit inter-satellite links (ISLs). To reduce transmission delays, we further introduce tailored communication strategies that integrate both communication and computing resources. Specifically, we propose a parallel intra-orbit communication strategy, a topology-aware satellite-ground communication strategy, and a latency-minimalization inter-orbit communication strategy to reduce space communication costs. Simulation results demonstrate significant reductions in training time with improvements of approximately 33%.
Privacy-Preserving Distributed Link Predictions Among Peers in Online Classrooms Using Federated Learning
Venue: arXiv cs.SI 2025
Year: 2025

Social interactions among classroom peers, represented as social learning networks (SLNs), play a crucial role in enhancing learning outcomes. While SLN analysis has recently garnered attention, most existing approaches rely on centralized training, where data is aggregated and processed on a local/cloud server with direct access to raw data. However, in real-world educational settings, such direct access across multiple classrooms is often restricted due to privacy concerns. Furthermore, training models on isolated classroom data prevents the identification of common interaction patterns that exist across multiple classrooms, thereby limiting model performance. To address these challenges, we propose one of the first frameworks that integrates Federated Learning (FL), a distributed and collaborative machine learning (ML) paradigm, with SLNs derived from students' interactions in multiple classrooms' online forums to predict future link formations (i.e., interactions) among students. By leveraging FL, our approach enables collaborative model training across multiple classrooms while preserving data privacy, as it eliminates the need for raw data centralization. Recognizing that each classroom may exhibit unique student interaction dynamics, we further employ model personalization techniques to adapt the FL model to individual classroom characteristics. Our results demonstrate the effectiveness of our approach in capturing both shared and classroom-specific representations of student interactions in SLNs. Additionally, we utilize explainable AI (XAI) techniques to interpret model predictions, identifying key factors that influence link formation across different classrooms. These insights unveil the drivers of social learning interactions within a privacy-preserving, collaborative, and distributed ML framework -- an aspect that has not been explored before.
Poly-Vector Retrieval: Reference and Content Embeddings for Legal Documents
Venue: arXiv cs.IR 2025
Year: 2025

Retrieval-Augmented Generation (RAG) has emerged as an effective paradigm for generating contextually accurate answers by integrating Large Language Models (LLMs) with retrieval mechanisms. However, in legal contexts, users frequently reference norms by their labels or nicknames (e.g., Article 5 of the Constitution or Consumer Defense Code (CDC)), rather than by their content, posing challenges for traditional RAG approaches that rely solely on semantic embeddings of text. Furthermore, legal texts themselves heavily rely on explicit cross-references (e.g., "pursuant to Article 34") that function as pointers. Both scenarios pose challenges for traditional RAG approaches that rely solely on semantic embeddings of text, often failing to retrieve the necessary referenced content. This paper introduces Poly-Vector Retrieval, a method assigning multiple distinct embeddings to each legal provision: one embedding captures the content (the full text), another captures the label (the identifier or proper name), and optionally additional embeddings capture alternative denominations. Inspired by Frege's distinction between Sense and Reference, this poly-vector retrieval approach treats labels, identifiers and reference markers as rigid designators and content embeddings as carriers of semantic substance. Experiments on the Brazilian Federal Constitution demonstrate that Poly-Vector Retrieval significantly improves retrieval accuracy for label-centric queries and potential to resolve internal and external cross-references, without compromising performance on purely semantic queries. The study discusses philosophical and practical implications of explicitly separating reference from content in vector embeddings and proposes future research directions for applying this approach to broader legal datasets and other domains characterized by explicit reference identifiers.
Multi-Modal Hypergraph Enhanced LLM Learning for Recommendation
Venue: arXiv cs.IR 2025
Year: 2025

The burgeoning presence of Large Language Models (LLM) is propelling the development of personalized recommender systems. Most existing LLM-based methods fail to sufficiently explore the multi-view graph structure correlations inherent in recommendation scenarios. To this end, we propose a novel framework, Hypergraph Enhanced LLM Learning for multimodal Recommendation (HeLLM), designed to equip LLMs with the capability to capture intricate higher-order semantic correlations by fusing graph-level contextual signals with sequence-level behavioral patterns. In the recommender pre-training phase, we design a user hypergraph to uncover shared interest preferences among users and an item hypergraph to capture correlations within multimodal similarities among items. The hypergraph convolution and synergistic contrastive learning mechanism are introduced to enhance the distinguishability of learned representations. In the LLM fine-tuning phase, we inject the learned graph-structured embeddings directly into the LLM's architecture and integrate sequential features capturing each user's chronological behavior. This process enables hypergraphs to leverage graph-structured information as global context, enhancing the LLM's ability to perceive complex relational patterns and integrate multimodal information, while also modeling local temporal dynamics. Extensive experiments demonstrate the superiority of our proposed method over state-of-the-art baselines, confirming the advantages of fusing hypergraph-based context with sequential user behavior in LLMs for recommendation.
SPreV
Venue: arXiv cs.GR 2025
Year: 2025

SPREV, short for hyperSphere Reduced to two-dimensional Regular Polygon for Visualisation, is a novel dimensionality reduction technique developed to address the challenges of reducing dimensions and visualizing labeled datasets that exhibit a unique combination of three characteristics: small class size, high dimensionality, and low sample size. SPREV is designed not only to uncover but also to visually represent hidden patterns within such datasets. Its distinctive integration of geometric principles, adapted for discrete computational environments, makes it an indispensable tool in the modern data science toolkit, enabling users to identify trends, extract insights, and navigate complex data efficiently and effectively.
Improving In-Context Learning with Reasoning Distillation
Venue: arXiv cs.CL 2025
Year: 2025

Language models rely on semantic priors to perform in-context learning, which leads to poor performance on tasks involving inductive reasoning. Instruction-tuning methods based on imitation learning can superficially enhance the in-context learning performance of language models, but they often fail to improve the model's understanding of the underlying rules that connect inputs and outputs in few-shot demonstrations. We propose ReDis, a reasoning distillation technique designed to improve the inductive reasoning capabilities of language models. Through a careful combination of data augmentation, filtering, supervised fine-tuning, and alignment, ReDis achieves significant performance improvements across a diverse range of tasks, including 1D-ARC, List Function, ACRE, and MiniSCAN. Experiments on three language model backbones show that ReDis outperforms equivalent few-shot prompting baselines across all tasks and even surpasses the teacher model, GPT-4o, in some cases. ReDis, based on the LLaMA-3 backbone, achieves relative improvements of 23.2%, 2.8%, and 66.6% over GPT-4o on 1D-ARC, ACRE, and MiniSCAN, respectively, within a similar hypothesis search space. The code, dataset, and model checkpoints will be made available at https://github.com/NafisSadeq/reasoning-distillation.git.
Balanced TSP partitioning
Venue: arXiv cs.CG 2025
Year: 2025

The traveling salesman problem (TSP) famously asks for a shortest tour that a salesperson can take to visit a given set of cities in any order. In this paper, we ask how much faster $k \ge 2$ salespeople can visit the cities if they divide the task among themselves. We show that, in the two-dimensional Euclidean setting, two salespeople can always achieve a speedup of at least $\frac12 + \frac1π\approx 0.818$, for any given input, and there are inputs where they cannot do better. We also give (non-matching) upper and lower bounds for $k \geq 3$.
EMAFusion: A Self-Optimizing System for Seamless LLM Selection and Integration
Venue: arXiv cs.CL 2025
Year: 2025

While recent advances in large language models (LLMs) have significantly enhanced performance across diverse natural language tasks, the high computational and financial costs associated with their deployment remain substantial barriers. Existing routing strategies partially alleviate this challenge by assigning queries to cheaper or specialized models, but they frequently rely on extensive labeled data or fragile task-specific heuristics. Conversely, fusion techniques aggregate multiple LLM outputs to boost accuracy and robustness, yet they often exacerbate cost and may reinforce shared biases. We introduce EMAFusion, a new framework that self-optimizes for seamless LLM selection and reliable execution for a given query. Specifically, EMAFusion integrates a taxonomy-based router for familiar query types, a learned router for ambiguous inputs, and a cascading approach that progressively escalates from cheaper to more expensive models based on multi-judge confidence evaluations. Through extensive evaluations, we find EMAFusion outperforms the best individual models by over 2.6 percentage points (94.3% vs. 91.7%), while being 4X cheaper than the average cost. EMAFusion further achieves a remarkable 17.1 percentage point improvement over models like GPT-4 at less than 1/20th the cost. Our combined routing approach delivers 94.3% accuracy compared to taxonomy-based (88.1%) and learned model predictor-based (91.7%) methods alone, demonstrating the effectiveness of our unified strategy. Finally, EMAFusion supports flexible cost-accuracy trade-offs, allowing users to balance their budgetary constraints and performance needs.
Epistemic Uncertainty-aware Recommendation Systems via Bayesian Deep Ensemble Learning
Venue: arXiv cs.IR 2025
Year: 2025

Recommending items to users has long been a fundamental task, and studies have tried to improve it ever since. Most well-known models commonly employ representation learning to map users and items into a unified embedding space for matching assessment. These approaches have primary limitations, especially when dealing with explicit feedback and sparse data contexts. Two primary limitations are their proneness to overfitting and failure to incorporate epistemic uncertainty in predictions. To address these problems, we propose a novel Bayesian Deep Ensemble Collaborative Filtering method named BDECF. To improve model generalization and quality, we utilize Bayesian Neural Networks, which incorporate uncertainty within their weight parameters. In addition, we introduce a new interpretable non-linear matching approach for the user and item embeddings, leveraging the advantages of the attention mechanism. Furthermore, we endorse the implementation of an ensemble-based supermodel to generate more robust and reliable predictions, resulting in a more complete model. Empirical evaluation through extensive experiments and ablation studies across a range of publicly accessible real-world datasets with differing sparsity characteristics confirms our proposed method's effectiveness and the importance of its components.